A lot of these problems of publication order vs timeline order come from us reading them out of time, with the full benefit of retrospective hindsight- I know Thande points this out obliquely in the article, but arguably the only reason we can notice problems like this is because these novels are more widely read over a longer period of time than probably every non-franchise Stackpole, Zahn, and Allston novel combined. For authors who are likely way more used to readers following their books on a much smaller scale, without as much editorial guidance regarding timelines or continuity, where most of the people you want to sell to will buy their copy within a year, a lot of these problems disappear. Indeed, I recall seeing cheesy internal references exactly like the ones called out here in books by other prolific authors (personally thinking of a line in a Dean Koontz book where a place from a different book shows up on a hat used as part of an ISO standard Marvel type cap-jacket disguise, but other brands are available).
This is probably too many words to make too small a point, but I do feel like most of these problems (as they relate to the SW EU specifically, at least) result more from sci fi authors used to one publication model being airdroped into something totally different and doing the best they can to be clever and witty in a way that appeals more to fans following along directly than those of us who come back and see it years, decades later.
(Complete sidebar: I recently discovered Michael Stackpole gave Kevin J. Anderson his first fiction-writing-for-pay assignment; I don't know how well they maintained their relationship but I imagine the pill of retcon might have been easier to swallow for KJA with Stackpole on the byline.)